encode-toolkit

Skill · npm · ★ 22 · graded 2026-10-24Source linked

MCP server and Claude Code plugin for the ENCODE Project: search, download and analyze ChIP-seq, ATAC-seq, RNA-seq, WGBS, Hi-C and CUT&RUN data with 20 tools, 47 skills and 7 Nextflow pipelines

No outside reports on file

encode-toolkit is distributed via npm (encode-toolkit); review its source code, dependencies, and requested permissions before use.

Based on public adoption and transparency signals as of Oct 24, 2026. Our opinion, not a code audit or security guarantee.

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What it can access

Local filesNo local folder access notedLOW
Command executionRuns shell or system commandsREVIEW
Network reachConnects to outside service APINOTED
CredentialsNo API token requiredLOW
Package sourcenpm (encode-toolkit)PUBLIC

Inferred from this listing’s public package details and description. Check the project’s source before installing.

Install

npx -y encode-toolkit

All setup options ↓

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Everything known

We found nothing about this project in the sources we read (last checked 2026-10-30). That does not mean it has no problems.

0 incidents · 0 advisories · 0 news articles · 0 community threads · checked 2026-10-30

Popularity grade: C (from public signals such as stars and downloads, not a code review). Graded 2026-10-24.

Sources we read: OSV, GitHub Advisory Database, CISA Known Exploited Vulnerabilities, 44 security news feeds and our incident library. Last checked 2026-10-30.

Check a specific version →

About Encode Toolkit

Encode Toolkit is an agent skill focused on Developer tools and Data & databases: MCP server and Claude Code plugin for the ENCODE Project: search, download and analyze ChIP-seq, ATAC-seq, RNA-seq, WGBS, Hi-C and CUT&RUN data with 20 tools, 47 skills and 7 Nextflow pipelines.

It is published on npm as encode-toolkit and published on PyPI as encode-toolkit and hosted on GitHub at ammawla/encode-toolkit (21 GitHub stars, 32 weekly npm downloads). Based on its public metadata, it operates with standard local or API scope without broad shell execution flags noted.

Setup

Check these steps against the project’s own instructions before running anything.

Install the npm package encode-toolkit with post-install scripts disabled:

bash

npm install --ignore-scripts encode-toolkit

Review the upstream instructions at https://github.com/ammawla/encode-toolkit (opens external site) before enabling in your agent workspace.

Why this grade

CC — Moderate risk signals

Signal-based grade (2/7 points): listed in several sources, public source code. This reflects adoption and transparency, not a code review.

Popularity and upkeep

35/100

GitHub stars: 22
Weekly npm downloads: 32
Listing last refreshed: 2026-10-29

These are public popularity signals, not a maintenance check. Look at the repository’s commit history and open issues.

Risks to watch for

Dependency & version pinning: Distributed via npm (encode-toolkit). Pin an exact release version or commit SHA rather than floating tags so upstream updates are reviewed first.

How to lower the risk

Least-privilege permissions

Give it access only to the specific folders, accounts or projects it needs, never your whole drive or admin account.
Use a separate, limited API key or login just for this tool so you can switch it off without affecting anything else.

Network isolation

Run it on a work computer or sandbox account, not one holding personal or company-sensitive data.
If your IT team can, limit which websites and services it is allowed to contact.

Monitoring

Check its activity history or logs weekly at first, and look at what it changed or sent.
Turn on alerts for new logins or unusual usage on any account it connects to.

Red flags to watch for

It asks for more access than its job requires, or prompts you to paste passwords.
It suddenly updates with new owners, or starts contacting unfamiliar websites.

Questions

How do I install Encode Toolkit?

Install Encode Toolkit with npm install encode-toolkit or run it directly with npx -y encode-toolkit. For agent integration and configuration flags, see the documentation at github.com/ammawla/encode-toolkit. Pin an exact version and pass --ignore-scripts if you want to block post-install hooks.

Are there security reports about Encode Toolkit?

No reports found for this package in our research (last checked 2026-10-30). Encode Toolkit currently holds Grade C (Moderate risk signals) based on public adoption and transparency signals. Key risk areas to watch include dependency & version pinning:.

Is Encode Toolkit actively maintained?

Encode Toolkit has 22 GitHub stars and 32 weekly npm downloads. Our directory data was last refreshed on 2026-10-29. Check recent commit activity, release tags, and open issues at github.com/ammawla/encode-toolkit before pinning it in production.

What are alternatives to Encode Toolkit?

You can compare Encode Toolkit side by side with other Search skills in the Related tools section on this page, or use the Compare tool on AgentArmorHQ.

Maintain or use Encode Toolkit? Show its live grade in your GitHub README, docs site, or run a check from the terminal before you install.

AgentArmorHQ Risk Grade C for Encode Toolkit

GitHub README Markdown:

markdown

[![AgentArmorHQ Risk Grade for Encode Toolkit](https://agentarmorhq.com/api/badge/ammawla-encode-toolkit)](https://agentarmorhq.com/skills/ammawla-encode-toolkit)

HTML embed:

html

<a href="https://agentarmorhq.com/skills/ammawla-encode-toolkit"><img src="https://agentarmorhq.com/api/badge/ammawla-encode-toolkit" alt="AgentArmorHQ Risk Grade for Encode Toolkit" height="20" /></a>

Terminal check:

terminal

curl -fsSL https://agentarmorhq.com/api/cli | node --input-type=module - check "ammawla-encode-toolkit"

Share with your security lead

Need sign-off to use encode-toolkit? Copy this note for Slack, a ticket or a pull request.

### AgentArmorHQ Security Review Memo: encode-toolkit
- **Listing URL:** https://agentarmorhq.com/skills/ammawla-encode-toolkit
- **Type:** AI agent skill
- **Risk Grade:** Grade C (Moderate risk signals)
- **Outside Security Advisories on File:** 0
- **Public Adoption:** 22 GitHub stars, 32 weekly npm downloads

#### Permission & Blast-Radius Signals
- **Local files:** No local folder access noted
- **Command execution:** Runs shell or system commands
- **Network reach:** Connects to outside service API
- **Credentials:** No API token required
- **Package source:** npm (encode-toolkit)

#### Recommended Hardened Setup
- **Command:** `npx -y --ignore-scripts encode-toolkit`
- **Controls:** Pin an exact version in `.mcp.json`, scope access to a single workspace folder, and use a least-privilege read-only token where supported.

_Based on public adoption and transparency signals as of Oct 24, 2026. Our opinion, not a code audit or security guarantee._

Key facts

Type: AI agent skill
Publisher: ammawla
Source code: github.com/ammawla/encode-toolkit
Install command: npm install encode-toolkit
Est. context load: ~76 tokens idle · ~450 tokens when active (on-demand skill)
Popularity: 22 GitHub stars, 32 weekly npm downloads
Last updated: 2026-10-29
Last graded: 2026-10-24

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